[REVIEW]: Analysing 24-hour behaviour sequence data with an Rshiny application

whedon commented 4 years ago

Submitting author: @jcolomb (Colomb, J.) Repository: https://github.com/jcolomb/HCS_analysis Version: v0.1.3 Editor: @danielskatz Reviewer: @mikerspencer, @aj2duncan Archive: Pending

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mikerspencer & @aj2duncan, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @mikerspencer

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jcolomb) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @aj2duncan

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jcolomb) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mikerspencer, @aj2duncan it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

👋 @mikerspencer & @aj2duncan - thanks again for agreeing to review this submission. Please be sure to read the comments above, and let me know if you have any questions. Basically, your job is to check the article proof and repository and check items off your checklist above.

If you see small problems that need to be discussed, feel free to discuss them here. But if you can, create a new issue in the target repository and link to this review thread in that issue to create corresponding breadcrumb trail here.

I look forward to seeing how this review goes!

mikerspencer commented 4 years ago

@danielskatz to be clear - @aj2duncan and I work together a little. Reviewers working together isn't specifically mentioned in the conflict of interest, but I feel it's best to be transparent.

danielskatz commented 4 years ago

Thanks for letting me know. This isn't 100% ideal, but given that you both likely have different backgrounds and experiences, and we're focusing on a checklist-driven process, it should be ok. Let's see how it goes.

aj2duncan commented 4 years ago

Thanks @mikerspencer and apologies @danielskatz, I should have raised this too. I'm happy to provide more detail on this if needed and I'm pretty sure @mikerspencer would be too.

danielskatz commented 4 years ago

👋 @jcolomb - it looks like there's an issue blocking @mikerspencer ..

@aj2duncan & @mikerspencer - how are your reviews coming along otherwise?

aj2duncan commented 4 years ago

@danielskatz now @jcolomb has confirmed a particular part of the installation isn't necessary I will push on with the review.

danielskatz commented 4 years ago

Thanks - please make sure the documentation matches what you learn

danielskatz commented 4 years ago

👋 @aj2duncan & @mikerspencer - how are your reviews doing?

aj2duncan commented 4 years ago

@jcolomb quick query - In the shiny app and article you make reference to the 18 Berlin categories. Should this have a reference?

jcolomb commented 4 years ago

no, this is a "in-house" categorisation that was (so far) not published.

aj2duncan commented 4 years ago

no, this is a "in-house" categorisation that was (so far) not published.

Thanks for the clarification.

danielskatz commented 4 years ago

👋 @aj2duncan & @mikerspencer - I'm just checking on your reviews and their progress again...

aj2duncan commented 4 years ago

@danielskatz everything seems to be moving along ok for me.

mikerspencer commented 4 years ago

@danielskatz can I check the scope of the review? How involved should we be as reviewers? I think testing should be done prior to review, but realise that's a grey area on problems picked up in the review.

danielskatz commented 4 years ago

@mikerspencer - I don't think I understand what you are asking. You should do as much as possible to verify the criteria in the checklist, subject to reasonable effort, and then report what problems you come across so that the submitter can respond. I'm confused when you say "I think testing should be done prior to review" There should be some tests provided by the submitter (either manual or via some script or something else), and part of your job is to verify that they work and that you think they are reasonable, given the software, and the JOSS documentation about testing

Let me know if this helps, and if not, please ask me again.

mikerspencer commented 4 years ago

Thanks @danielskatz your comment on verification is helpful. I think working on this issue (https://github.com/jcolomb/HCS_analysis/issues/18) is becoming more like co-creation. Keen to have your experienced view!

danielskatz commented 4 years ago

Well, ideally everything should work for the reviewer when they first try it, but if that was guaranteed, we wouldn't need any reviews :)

So, yes, sometimes the reviewers will work with the author to test things and this can be somewhat iterative. If it's too much work, you can ask the author to go off and test with colleagues and come back when they are fairly sure the tests will pass for the reviewers, but sometimes, there is something tricky that does need to be worked out between reviewers and authors too.

Thanks for your help in doing this, and getting this far.

mikerspencer commented 4 years ago

No problem, thanks for clarifying - I appreciate it's a fine line!

@aj2duncan has done most of the work so far I think.

danielskatz commented 4 years ago

👋 @aj2duncan & @mikerspencer - As we're now almost 2 months into the review process, can you each please tell me:

Are you waiting on @jcolomb for anything?
If so, for what?
if not, when do you expect your review to be complete?

aj2duncan commented 4 years ago

Hi @danielskatz,

I'm waiting on jcolomb/HCS_analysis#20 and then I've got a couple of documentation things to check. I hope to have this done over the weekend.

aj2duncan commented 4 years ago

@danielskatz question for you.

I think a statement of need is missing from the github repo but is present in the paper and @jcolomb has linked the paper from the first section of the README. Could you please comment on whether anything additional is required?

Thanks.

danielskatz commented 4 years ago

@danielskatz question for you.

I think a statement of need is missing from the github repo but is present in the paper and @jcolomb has linked the paper from the first section of the README. Could you please comment on whether anything additional is required?

Thanks.

It would probably be good to include some of this statement in the README directly.

danielskatz commented 4 years ago

👋 @jcolomb - how are you coming on the open issues?

jcolomb commented 4 years ago

I need some extra time. Sorry I can't be more reactive on this and thank you for the reminder !

danielskatz commented 4 years ago

👋 @jcolomb - another checkin - how are you coming on the open issues?

jcolomb commented 4 years ago

I am on it, probably get something showable this week.

jcolomb commented 4 years ago

hopefully done with the difficult parts, hope to finish tomorrow.

jcolomb commented 4 years ago

I am basically done, lots of debug and extension for online data in mbr format, documentation in readme and in metadata_information/readme were reworked quite a bit. Changes are in the https://github.com/jcolomb/HCS_analysis/tree/joss_reviewanswers branch, and comment may be done in the pull request https://github.com/jcolomb/HCS_analysis/pull/27

Thank you a lot for all the feedback and the patience.

danielskatz commented 4 years ago

@aj2duncan & @mikerspencer - back over to you

aj2duncan commented 4 years ago

Thanks @jcolomb and @danielskatz, will look at this again as soon as I can.

mikerspencer commented 4 years ago

Cheers!

danielskatz commented 4 years ago

Cheers!

Does that translate into American as "I'll get back to my review soon"? 🙂

aj2duncan commented 4 years ago

Hi @danielskatz, just to let you know that although there are a couple of small things to be ironed out I'll be done once we close jcolomb/HCS_analysis#20

aj2duncan commented 4 years ago

@danielskatz I think I've now finished my review. @jcolomb has dealt with all of my concerns. Thanks.

danielskatz commented 4 years ago

Thanks @aj2duncan!

danielskatz commented 4 years ago

👋 @mikerspencer - How is you review coming? That's what we need to move forward, either to accept or to figure out what needs to be changed.

danielskatz commented 4 years ago

👋 @mikerspencer - How is your review coming? Can you give us some idea when you might expect to complete it?

mikerspencer commented 4 years ago

Hi @danielskatz, apologies for the radio silence. I'm in the last two weeks of my current job, so things are a little frantic finishing tasks and tidying loose ends.

I will have more time from the 12th Oct, are you OK to wait until then?

danielskatz commented 4 years ago

Ok, we can wait until then (since trying to bring in another reviewer would likely be equally as long)

danielskatz commented 4 years ago

@whedon remind @mikerspencer in 17 days

whedon commented 4 years ago

Reminder set for @mikerspencer in 17 days

mikerspencer commented 4 years ago

Many thanks - unfortunately life has overtaken me this time!

whedon commented 4 years ago

:wave: @mikerspencer, please update us on how your review is going.

mikerspencer commented 4 years ago

Hi, thanks for the check in. Should be finished tomorrow.

mikerspencer commented 4 years ago

I've paused my review while I wait for this issue to be fixed: https://github.com/jcolomb/HCS_analysis/issues/30.

danielskatz commented 4 years ago

@jcolomb - any update on this issue ⬆️ ?

jcolomb commented 4 years ago

It was fixed (I hope), sorry forgot to mention it here.

danielskatz commented 4 years ago

👋 @mikerspencer - see https://github.com/jcolomb/HCS_analysis/issues/30#issuecomment-718730338

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